Searching journal content for articles similar to Ono et al. 13 (7): 1696.

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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...gene receptor clusters found within this region (Giglio et al. 2001). Individuals affected by 8p syndrome present with a variety of clinical phenotypes, including agenesis of the corpus callosum, epilepsy, and other neurodevelopmental delays (Vibert et al. 2022).Over the past several decades...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...correlation coefficient higher than 0.7. (D) Heatmap showing the normalized expression level detected in RNA sequencing data sets for host and nested gene pairs with a Spearman's rank correlation coefficient higher than 0.7. Host genes were clustered using hierarchical clustering according to their expression...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...regulation. By critically examining both established tools and emerging techniques such as editing, synthetic chromosomes, and high-resolution imaging, we provide a practical framework for investigators seeking to uncover direct regulators of specific genes. Our goal is to guide the design of experiments...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...in mice housing the α-globin gene cluster, delineate the chromatin region where enhancers gain access and interact with responsive promoters, which underscored the association of hierarchical TADs with gene-specific regulation. Moreover, several studies have documented a category of partially overlapping...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...families based on their functions, including maltose transporter (MALT), enzymes that break down maltose (MALS), and genes that regulate the expression of the pathway (MALR). These genes are often organized into clusters and located near the ends of chromosomes (subtelomeric). To elucidate the origins...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...the . CpG loci tend to be found in dense clusters in gene promoters called CpG islands (CGIs), and differential methylation of these CGIs plays an important role in gene regulation (Schmitz et al. 2019). Although this relationship between CGI methylation and gene expression regulation is thought...
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Research: Pervasive polymorphic imprinted methylation in the human placenta
- Courtney W. Hanna,
- Maria S. Peñaherrera,
- Heba Saadeh,
- Simon Andrews,
- Deborah E. McFadden,
- Gavin Kelsey,
- and Wendy P. Robinson
Genome Res. June 2016 26: 756-767; Published in Advance January 14, 2016, doi:10.1101/gr.196139.115
...) and the Chromosome 19 microRNA cluster (C19MC) (Noguer-Dance et al. 2010). There are also examples of loci where biallelic expression has been documented despite a nearby imprinted DMR, such as at RASGRF1 and C3orf62 (Yuen et al. 2011a). This suggests that additional factors may be important for imprinted gene...
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Research: Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming
- Adrian Janiszewski,
- Irene Talon,
- Joel Chappell,
- Samuel Collombet,
- Juan Song,
- Natalie De Geest,
- San Kit To,
- Greet Bervoets,
- Oskar Marin-Bejar,
- Caterina Provenzano,
- Lotte Vanheer,
- Jean-Christophe Marine,
- Florian Rambow,
- and Vincent Pasque
Genome Res. October 2019 29: 1659-1672; Published in Advance September 12, 2019, doi:10.1101/gr.249706.119
...and repressive protein complexes and are located within residual TAD-like clusters on the Xi (Balaton and Brown 2016; Giorgetti et al. 2016). XCI, therefore, provides a paradigmatic example of chromosome-wide gene silencing stably maintained in somatic cells. The precise relationship between epigenetic...
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Research: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
- Celine L. St. Pierre,
- Juan F. Macias-Velasco,
- Jessica P. Wayhart,
- Li Yin,
- Clay F. Semenkovich,
- and Heather A. Lawson
Genome Res. June 2022 32: 1042-1057; Published in Advance May 2, 2022, doi:10.1101/gr.276193.121
...-nine genes were canonically imprinted (bolded in Fig. 3, defined in Methods), and the other 169 genes were various noncoding RNAs located within known imprinted domains. For example, 156 genes were in a cluster of 171 paternally biased snoRNAs in the PWS/AS domain on Chromosome 7 (Supplemental Fig. S3...
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Research: A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation
- Hala Al Adhami,
- Brendan Evano,
- Anne Le Digarcher,
- Charlotte Gueydan,
- Emeric Dubois,
- Hugues Parrinello,
- Christelle Dantec,
- Tristan Bouschet,
- Annie Varrault,
- and Laurent Journot
Genome Res. March 2015 25: 353-367; Published in Advance January 22, 2015, doi:10.1101/gr.175919.114
...of expressionwasmost dissimilar to that of IGs, displayed the exact reverse behavior (Fig. 6E). Discussion Parental genomic imprinting has commanded attention over the past three decades as a prototypical epigenetic gene regulation mechanism. The identification of mechanisms governing parentof...
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